mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
James Taylor
bb769367ed
configured at the application level. Specific tabular data files are specified in a application config file and bound to names, the tools then refer to these names. Thus users can configure where location files are located without modifying tool configs. Also: - Simpler column name configuration - Columns can be referred to by name in addition to index in all dynamic option filters - A data table can merge multiple files - Design can support other types of data files
64 lines
1.4 KiB
Bash
64 lines
1.4 KiB
Bash
#!/bin/sh
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python ./scripts/check_python.py
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[ $? -ne 0 ] && exit 1
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SAMPLES="
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datatypes_conf.xml.sample
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reports_wsgi.ini.sample
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tool_conf.xml.sample
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tool_data_table_conf.xml.sample
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universe_wsgi.ini.sample
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tool-data/alignseq.loc.sample
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tool-data/annotation_profiler_options.xml.sample
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tool-data/annotation_profiler_valid_builds.txt.sample
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tool-data/binned_scores.loc.sample
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tool-data/blastdb.loc.sample
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tool-data/bowtie_indices.loc.sample
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tool-data/encode_datasets.loc.sample
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tool-data/liftOver.loc.sample
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tool-data/maf_index.loc.sample
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tool-data/maf_pairwise.loc.sample
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tool-data/microbial_data.loc.sample
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tool-data/phastOdds.loc.sample
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tool-data/quality_scores.loc.sample
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tool-data/regions.loc.sample
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tool-data/sam_fa_indices.loc.sample
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tool-data/sequence_index_base.loc.sample
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tool-data/sequence_index_color.loc.sample
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tool-data/twobit.loc.sample
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tool-data/shared/ucsc/builds.txt.sample
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"
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DIRS="
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database
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database/files
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database/community_files
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database/tmp
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database/compiled_templates
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database/job_working_directory
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database/import
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database/pbs
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static/genetrack/plots
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tool-data/shared/jars
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"
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for sample in $SAMPLES; do
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file=`echo $sample | sed -e 's/\.sample$//'`
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if [ -f $file ]; then
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echo "Not overwriting existing $file"
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else
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echo "Copying $sample to $file"
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cp $sample $file
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fi
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done
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for dir in $DIRS; do
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if [ ! -d $dir ]; then
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echo "Creating $dir"
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mkdir $dir
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fi
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done
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python ./scripts/fetch_eggs.py
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